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The Wold Lab BioHub Cory Tobin Collaborators Brandon King Joe Roden Diane Trout Dr. Barbara Goal • Standardize the relationship between biological data • Integrate all of the data seamlessly • Provide novel methods to search for and analyze data Adapted from http://woldlab.caltech.edu/biohub/ My Contribution Implement a database for homology data Background Species A Gene Gene Paralogs The more general term is “homology” Orthologs Species B Gene Requirements • Be more accurate and flexible than HomoloGene • Work in real time • Make sense of HomoloGene’s misleading data Rationale BioHub HomoloGene Gene Gene Gene Gene Gene Gene Gene Gene Gene Gene They are similar They are related like this Rationale Continued Seq A Seq B Human Genome BioHub will BLAST A BLAST against HomoloGene wouldseq BLAST also seq mouse, find seq C, then BLAST C A against seq B against mouse mouse and and determine back against human to an see that seq detrmine Cthat is an seq ortholog C is of ifseq there areof any matches. It A. ortholog seqbetter B. will find seq B to be better. Seq C Mouse Genome Methods • Design data relationships that make sense biologically • Generate the low-level database interaction code • Parse and load HomoloGene’s data into our database • Write biologically useful functions • Create a web-based interface for easy use Materials • ArgoUML – Design Aid • Pymerase – Design Implementation • PostgreSQL – Database • HomoloGene – Data Source • Python – Programming Language Current State • Design data relationships that make sense biologically • Generate the low-level database interaction code • Parse and load HomoloGene’s data into our database • Write biologically useful functions • Create a web-based interface for easy use Example Usage Sequence of Interest …GGATACAAAATTCCTC… Are there any known genes in this sequence? acetyl - coenzyme A dehydrogenase ( Human ) (cont.) acetyl - coenzyme A dehydrogenase ( Human ) Are there any homologs? Mouse Rat Mosquito Fruit fly Nematode (cont.) How are those genes related? Where do you want to go? More Info BioHub woldlab.caltech.edu / biohub HomoloGene www.ncbi.nlm.nih.gov Python python.org Pymerase pymerase.sf.net PostgreSQL postgresql.org